vonHoldt Lab

Evolutionary Genomics and Ecological Epigenomics

Ecological Epigenomics. Wild species can exhibit numerous phenotypes, some of which have been locally adapted, often classified as ecotypes or perhaps subspecies supported by genetic evidence. Any species with a large geographic distribution, often spanning a variety of ecologies (e.g. arid, boreal forest, arctic) can be the focus of exploring how habitat gradients and genetics are correlated, often under the hypothesis focused on genes that are locally adapted. Across said gradients, populations can be highly differentiated with fine-scale genetic structuring and phenotype variation. Analysis of the methylome can provide a unique opportunity to address ecological/evolutionary questions regarding adaptation and response to selection: What degree of natural epigenetic variation exists? Do patterns of methylation segregate with locally adapted populations or overlap with known locally adapted loci? Do transposition-methylation dynamics correlate with fine-scale population structure? How do phenotypes and methylation patterns segregate? Further, I can survey variation in the regulatory genome in relation to specific phenotypes (e.g. body size, skeletal proportions, coat color), social rank (e.g. stress, aggression), demography (e.g. inbreeding), or evolutionary history (e.g. domesticated species, highly inbred or genetically isoalted). (Collaborators: Drs. Daniel Stahler and Douglas Smith of the Yellowstone Wolf Recovery Project; Drs. Robert Wayne, Matteo Pellegrini, and Thomas Smith at UCLA; Dr. Marco Musiani at University of Calgary)

Transposon dynamics of domesticated and wild canids.Strong artificial selection of domestication and recent selective breeding of dogs has targeted specific genetic variants of large effect (e.g. coloration, skeletal proportions). Along with many variants at the DNA level, other dimensions of the genome have likely been shaped by artificial selection. Transposons are mobile DNA elements that can amplify independently of the host genome, with their insertion locations potentially influencing gene transcription. Most transposons are targeted for epigenetic silencing by the host defense system but some are likely to escape silencing. Insertions into regulatory regions or transposons that capture/duplicate functionally-important coding regions are expected to rapidly impact phenotypic diversity. These, among other genomic features, are the target of further genome analysis of wild and domesticated species. (Collaborators: Dr. Robert Wayne at UCLA)

Introgression analysis and admixture mapping. Closely-related species that readily hybridize are often the center of controversy over taxonomic status and priority for conservation management. Ancestry of potentially mixing populations is difficult to resolve when the parental species are closely related. Using a genome-wide approach across a geographic sampling of putatively admixed populations, resolving the ancestry assignment of genomic segments will assist in mapping out not only geographic hybrid zones (e.g. Great Lakes region for wolves and coyotes) but also estimate the timings of the initial admixture event.(Collaborators: Dr. Robert Wayne at UCLA, Dr. Roland Kays at the North Carolina Museum of Natural Sciences)

Yellowstone wolf pedigree and population genetic analyses. Analysis of additional wolves, integrating field-based observational data, in addition to pedigree-based inheritance analyses. Additionally, dispersal and population structure as the population recovers and hovers at capacity is an ongoing effort. (Collaborators: Drs. Daniel Stahler and Douglas Smith of the Yellowstone Wolf Recovery Project; Dr. Robert Wayne at UCLA)